update totake into account indels

lib/identical.ml

@@ -55,6 +55,9 @@ let conf_file_bppancestor ~tree ~faa ~out ~config =
       assign "OUT" (out) ;
       assign "input.sequence.file" (dep faa) ;
       assign "alphabet" (string "Protein") ;
+      assign "input.sequence.remove_stop_codons" (string "no") ;
+      assign "input.sequence.sites_to_use" (string "all") ;
+      assign "input.sequence.remove_saturated_sites" (string "yes") ;
 
       assign "input.tree.file"  (dep tree) ;
       assign "init.tree" (string "user") ;